1 |
<<<<<<< Bend.cpp |
2 |
#include "primitives/Bend.hpp" |
3 |
namespace oopse { |
4 |
|
5 |
/**@todo still a lot left to improve*/ |
6 |
void Bend::calcForce() { |
7 |
|
8 |
Vector3d pos1 = atom1_->getPos(); |
9 |
Vector3d pos2 = atom2_->getPos(); |
10 |
Vector3d pos3 = atom3_->getPos(); |
11 |
|
12 |
Vector3d r12 = pos1 - pos2; |
13 |
double d12 = r12.length(); |
14 |
double d12inv = 1. 0 / d12; |
15 |
|
16 |
Vector3d r32 = pos3 - pos2; |
17 |
double d32 = r32.length(); |
18 |
double d32inv = 1. 0 / d32; |
19 |
|
20 |
double cosTheta = (r12*r32)/(d12*d32); |
21 |
|
22 |
//check roundoff |
23 |
if (cosTheta > 1.0) { |
24 |
cosTheta = 1.0; |
25 |
} else if (cosTheta < -1.0) { |
26 |
cosTheta = -1.0; |
27 |
} |
28 |
|
29 |
double theta = acos(cosTheta); |
30 |
|
31 |
double firstDerivative; |
32 |
|
33 |
bendType_->calcForce(theta, firstDerivative, potential_); |
34 |
|
35 |
double sinTheta = sqrt(1.0 - cosTheta*cosTheta); |
36 |
|
37 |
if(fabs(sinTheta) < 1.0E-12 ) { |
38 |
sinTheta = 1.0E-12; |
39 |
} |
40 |
|
41 |
double commonFactor1 = - firstDerivative / sinTheta * d12inv; |
42 |
double commonFactor2 = - firstDerivative / sinTheta * d32inv; |
43 |
|
44 |
Vector3d force1 = commonFactor1*(r12*(d12inv*cosTheta) - r32*d32inv); |
45 |
Vector3d force3 = commonFactor2*(r32*(d32inv*cosTheta) - r12*d12inv); |
46 |
|
47 |
//total force in current bend is zero |
48 |
Vector3d force2 = force1 + force3; |
49 |
force2 *= -1.0; |
50 |
|
51 |
atom1_->addFrc( force1); |
52 |
atom2_->addFrc(force2); |
53 |
atom3_->addFrc(force3); |
54 |
|
55 |
} |
56 |
|
57 |
double k = value->k * scale; |
58 |
double theta0 = value->theta0; |
59 |
|
60 |
double diff = theta - theta0; |
61 |
|
62 |
double energy = k *diff*diff; |
63 |
|
64 |
double firstDerivative = 2.0 * k * diff; |
65 |
|
66 |
}//end namespace oopse |
67 |
======= |
68 |
#include "primitives/Bend.hpp" |
69 |
|
70 |
namespace oopse { |
71 |
|
72 |
/**@todo still a lot left to improve*/ |
73 |
void Bend::calcForce() { |
74 |
Vector3d pos1 = atom1_->getPos(); |
75 |
Vector3d pos2 = atom2_->getPos(); |
76 |
Vector3d pos3 = atom3_->getPos(); |
77 |
|
78 |
Vector3d r12 = pos1 - pos2; |
79 |
double d12 = r12.length(); |
80 |
|
81 |
double d12inv = 1.0 / d12; |
82 |
|
83 |
Vector3d r32 = pos3 - pos2; |
84 |
double d32 = r32.length(); |
85 |
|
86 |
double d32inv = 1.0 / d32; |
87 |
|
88 |
double cosTheta = dot(r12, r32) / (d12 * d32); |
89 |
|
90 |
//check roundoff |
91 |
if (cosTheta > 1.0) { |
92 |
cosTheta = 1.0; |
93 |
} else if (cosTheta < -1.0) { |
94 |
cosTheta = -1.0; |
95 |
} |
96 |
|
97 |
double theta = acos(cosTheta); |
98 |
|
99 |
double firstDerivative; |
100 |
|
101 |
bendType_->calcForce(theta, firstDerivative, potential_); |
102 |
|
103 |
double sinTheta = sqrt(1.0 - cosTheta * cosTheta); |
104 |
|
105 |
if (fabs(sinTheta) < 1.0E-12) { |
106 |
sinTheta = 1.0E-12; |
107 |
} |
108 |
|
109 |
double commonFactor1 = -firstDerivative / sinTheta * d12inv; |
110 |
double commonFactor2 = -firstDerivative / sinTheta * d32inv; |
111 |
|
112 |
Vector3d force1 = commonFactor1*(r12*(d12inv*cosTheta) - r32*d32inv); |
113 |
|
114 |
Vector3d force3 = commonFactor2*(r32*(d32inv*cosTheta) - r12*d12inv); |
115 |
|
116 |
//total force in current bend is zero |
117 |
Vector3d force2 = force1 + force3; |
118 |
force2 *= -1.0; |
119 |
|
120 |
atom1_->addFrc(force1); |
121 |
atom2_->addFrc(force2); |
122 |
atom3_->addFrc(force3); |
123 |
} |
124 |
|
125 |
} //end namespace oopse |
126 |
>>>>>>> 1.2.2.4 |